Load - Revision history

Cchem: 1 revision

2018-01-08T04:03:24Z

1 revision

Speleo3: ARGUMENTS

2018-01-03T14:15:22Z

ARGUMENTS

Bell: 20 revisions

2015-04-21T22:50:01Z

20 revisions

Sbliven: Adding argument explainations

2015-03-18T14:00:30Z

Adding argument explainations

Pyadmin: 1 revision

2014-03-28T02:16:30Z

1 revision

Jaredsampson: /* SEE ALSO */

2013-11-21T14:42:08Z

MartinHediger: /* User Comments/Examples */

2012-01-23T15:17:52Z

User Comments/Examples

MartinHediger: /* User Comments/Examples */

2012-01-23T15:17:20Z

User Comments/Examples

New page

'''load''' reads several file formats. The file extension is used to determine the format. PDB files must end in ".pdb", MOL files must end in ".mol", Macromodel files must end in ".mmod", XPLOR maps must end in ".xplor", CCP4 maps must end in ".ccp4", Raster3D input (Molscript output) must end in ".r3d", PyMOL session files must end in ".pse", and pickled ChemPy models with a ".pkl" can also be directly read.

If an object is specified, then the file is loaded into that object. Otherwise, an object is created with the same name as the file prefix.

===USAGE===
<source lang="python">
load filename [,object [,state [,format [,finish [,discrete [,multiplex ]]]]]]
</source>

===PYMOL API===
<source lang="python">
cmd.load( filename [,object [,state [,format [,finish [,discrete [,multiplex ]]]]]] )
</source>

===NOTES===
*You can override the file extension by giving a format string:

'pdb' : PDB, 'mmod' : Macromodel, 'xyz' : Tinker, 'cc1' : ChemDraw3D
'mol' : MDL MOL-file, 'sdf' : MDL SD-file
'xplor' : X-PLOR/CNS map, 'ccp4' : CCP4 map,
'callback' : PyMOL Callback object (PyOpenGL)
'cgo' : compressed graphics object (list of floats)
'trj' : AMBER trajectory (use load_traj command for more control)
'top' : AMBER topology file 'rst' : AMBER restart file
'cex' : Metaphorics CEX format
'pse' : PyMOL Session file
'pqr' : PQR (a modified PDB file with charges and radii)
'mol2' : MOL2

* A new feature has been added to load. You can specify an URL to a PDB and PyMOL will download it. This is a very handy feature for loading experimental/theoretical data from servers across the web. Just copy the link they give you and do,
<source lang="python">
load http://www.theurl.com/path/toYourData
</source>
or you can open a remote file just from the command line
<source lang="bash">
# load a PDB file; I placed one example file on the PyMOL Wiki
pymol http://www.pymolwiki.org/1rsy.pdb

# PyMOL can also handle the gzipped files on the PDB. :-)
pymol ftp://ftp.wwpdb.org/pub/pdb/data/structures/divided/pdb/00/pdb100d.ent.gz
</source>

===User Comments/Examples===
*Load xyz.pdb using the PyMOL API:
<source lang="python">
cmd.load("xyz.pdb")
</source>

* Loading multiple PDBs into one object with many states:
<source lang="python">
load trj0001.pdb, mov
load trj0002.pdb, mov
load trj0003.pdb, mov
etc.
</source>
or, if you have too many states to do that by hand,
<source lang="python">
for idx in range(1,1001):cmd.load("trj%04d.pdb"%idx,"mov")
</source>
or, you can use "glob" from Python,
<source lang="python">
from glob import glob
lst = glob("trj*.pdb")
lst.sort()
for fil in lst: cmd.load(fil,"mov")
</source>

*Load a NAMD multi-PDB file. These are just concatenated PDB files.
<source lang="python">
load NAMDtrajFile.pdb, multiplex=0
</source>

* Hint: You can save some time & a lot of memory by loading the file and removing the atoms in a single-line compound statement (with a semicolon
after the load statement).
<source lang="python">
load 1E3M.pdb; remove not A-C+F//
</source>

* Decorating the load command to include technical info about the loaded object
<source>
def load_with_props(fileName, objName):
# store whatever info you want, like the filename
obj_info[objName] = fileName
# ... do more recording of properties you choose
# ask PyMOL to now load the file
cmd.load(fileName,objName)
</source>
Then on can query obj_info based on the object name:
<source>
for obj in cmd.get_names():
print obj_info[obj]
</source>

===SEE ALSO===
[[Save]] [[Load Traj]]

[[Category:Commands|Load]]
[[Category:States|Load]]
[[Category:Input Output Module|Load]]

Vinnyrose at 14:55, 20 June 2009

2009-06-20T14:55:07Z

Vinnyrose at 14:13, 20 June 2009

2009-06-20T14:13:11Z

New page

===DESCRIPTION===
'''load''' reads several file formats. The file extension is used to determine the format. PDB files must end in ".pdb", MOL files must end in ".mol", Macromodel files must end in ".mmod", XPLOR maps must end in ".xplor", CCP4 maps must end in ".ccp4", Raster3D input (Molscript output) must end in ".r3d", PyMOL session files must end in ".pse", and pickled ChemPy models with a ".pkl" can also be directly read.

If an object is specified, then the file is loaded into that object. Otherwise, an object is created with the same name as the file prefix.

===USAGE===
<source lang="python">
load filename [,object [,state [,format [,finish [,discrete [,multiplex ]]]]]]
</source>

===PYMOL API===
<source lang="python">
cmd.load( filename [,object [,state [,format [,finish [,discrete [,multiplex ]]]]]] )
</source>

===NOTES===
*You can override the file extension by giving a format string:

'pdb' : PDB, 'mmod' : Macromodel, 'xyz' : Tinker, 'cc1' : ChemDraw3D
'mol' : MDL MOL-file, 'sdf' : MDL SD-file
'xplor' : X-PLOR/CNS map, 'ccp4' : CCP4 map,
'callback' : PyMOL Callback object (PyOpenGL)
'cgo' : compressed graphics object (list of floats)
'trj' : AMBER trajectory (use load_traj command for more control)
'top' : AMBER topology file 'rst' : AMBER restart file
'cex' : Metaphorics CEX format
'pse' : PyMOL Session file
'pqr' : PQR (a modified PDB file with charges and radii)
'mol2' : MOL2

* A new feature has been added to load. You can specify an URL to a PDB and PyMOL will download it. This is a very handy feature for loading experimental/theoretical data from servers across the web. Just copy the link they give you and do,
<source lang="python">
load http://www.theurl.com/path/toYourData
</source>
or you can open a remote file just from the command line
<source lang="bash">
# load a PDB file; I placed one example file on the PyMOL Wiki
pymol http://www.pymolwiki.org/1rsy.pdb

# PyMOL can also handle the gzipped files on the PDB. :-)
pymol ftp://ftp.wwpdb.org/pub/pdb/data/structures/divided/pdb/00/pdb100d.ent.gz
</source>

===User Comments/Examples===
*Load xyz.pdb using the PyMOL API:
<source lang="python">
cmd.load("xyz.pdb")
</source>

* Loading multiple PDBs into one object with many states:
<source lang="python">
load trj0001.pdb, mov
load trj0002.pdb, mov
load trj0003.pdb, mov
etc.
</source>
or, if you have too many states to do that by hand,
<source lang="python">
for idx in range(1,1001):cmd.load("trj%04d.pdb"%idx,"mov")
</source>
or, you can use "glob" from Python,
<source lang="python">
from glob import glob
lst = glob("trj*.pdb")
lst.sort()
for fil in lst: cmd.load(fil,"mov")
</source>

*Load a NAMD multi-PDB file. These are just concatenated PDB files.
<source lang="python">
load NAMDtrajFile.pdb, multiplex=0
</source>

* Hint: You can save some time & a lot of memory by loading the file and removing the atoms in a single-line compound statement (with a semicolon
after the load statement).
<source lang="python">
load 1E3M.pdb; remove not A-C+F//
</source>

===SEE ALSO===
[[Save]] [[Load Traj]]

[[Category:Commands|Load]]
[[Category:States|Load]]

@@ Line 15: / Line 15: @@
 ===ARGUMENTS===
-* '''filename : string''' Path to the file to load.
+* '''filename : string''' Path or URL to the file to load.
 * '''object : string''' Name of Pymol object to store the structure in. Defaults to the filename prefix.
 * '''state : integer''' State number to store the object in, or 0 to append (default:0)
 * '''format : string''' Format for the file (see notes). Defaults to the filename extension.
 * '''finish : integer'''
-* '''discrete : integer''' For multi-model structures, a value of 0 indicates that models have the same set of atoms (e.g. trajectory files or NMR structures), allowing memory savings, while a value of 1 forces the creation of independent atom sets for each model
+* '''discrete : integer''' For multi-model structures, a value of 0 indicates that models have the same set of atoms (e.g. trajectory files or NMR structures), allowing memory savings, while a value of 1 forces the creation of independent atom sets for each model {default: -1 (file type dependent)} (see [[discrete objects]])
 * '''quiet : integer''' (default 1)
-* '''multiplex : integer'''
+* '''multiplex : integer''' Load a multi-model file as separate objects instead of states (see also [[split_states]])
-* '''zoom : integer'''
+* '''zoom : integer''' {default: -1 = use [[auto_zoom]] setting}
-* '''partial : integer''' (default 0)
+* '''partial : integer''' For session files (.pse). partial=0: discard current session. partial=1: merge with current session (will not load global settings, selections, movie, camera). partial=2: like 1, but also load camera view {default: 0}
-* '''mimic : integer''' (default 1)
+* '''mimic : integer''' For .mae files, match style from file as close as possible, uses atom-level settings (like [[cartoon_color]]) {default: 1}
 ===NOTES===

← Older revision		Revision as of 14:42, 21 November 2013
Line 94:		Line 94:

	===SEE ALSO===		===SEE ALSO===
−	[[Save]] [[Load Traj]]	+	[[Fetch]] [[Save]] [[Load Traj]]

← Older revision	Revision as of 04:03, 8 January 2018
(No difference)

← Older revision	Revision as of 22:50, 21 April 2015
(No difference)

@@ Line 1: / Line 1: @@
 '''load''' reads several file formats.  The file extension is used to determine the format.  PDB files must end in ".pdb", MOL files must end in ".mol", Macromodel files must end in ".mmod", XPLOR maps must end in ".xplor", CCP4 maps must end in ".ccp4", Raster3D input (Molscript output) must end in  ".r3d", PyMOL session files must end in ".pse", and pickled ChemPy models with a ".pkl" can also be directly read.
@@ Line 13: / Line 12: @@
 cmd.load( filename [,object [,state [,format [,finish [,discrete [,multiplex ]]]]]] )
 </source>
 ===NOTES===

← Older revision	Revision as of 02:16, 28 March 2014
(No difference)

@@ Line 79: / Line 79: @@
 * Decorating the load command to include technical info about the loaded object
-<source>
+<source lang="python">
 def load_with_props(fileName, objName):
    # store whatever info you want, like the filename
@@ Line 88: / Line 88: @@
 </source>
 Then on can query obj_info based on the object name:
-<source>
+<source lang="python">
 for obj in cmd.get_names():
    print obj_info[obj]

← Older revision		Revision as of 14:55, 20 June 2009
Line 84:		Line 84:
	[[Category:Commands\|Load]]		[[Category:Commands\|Load]]
	[[Category:States\|Load]]		[[Category:States\|Load]]
		+	[[Category:Input Output Module\|Load]]